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rdkit/Code/MinimalLib/tests/tests.js
Paolo Tosco 1bd39b2ad2 only test InChI functionality if it was built into JS MinimalLib (#7706) 
Co-authored-by: ptosco <paolo.tosco@novartis.com>
2024-08-13 06:02:49 +02:00

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//
//
// Copyright (C) 2019 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
const assert = require('assert');
const {
performance
} = require('perf_hooks');
// the default path to RDKit_minimal.js can be overridden through
// the RDKIT_MINIMAL_JS variable if needed
const minimalLib = process.env.RDKIT_MINIMAL_JS || '../demo/RDKit_minimal.js';
console.log('Loading ' + minimalLib);
var initRDKitModule = require(minimalLib);
var RDKitModule;
const fs = require('fs');
const readline = require('readline');
const extractBondCoords = (svg, bondDetail) => {
const getStartEndCoords = (bond) => {
const m = bond.match(/^.*\s+d='M\s+([^,]+),([^ ]+)\s+L\s+([^,]+),([^ ]+)'.*$/);
return [[m[1], m[2]], [m[3], m[4]]];
};
const bond = svg.split('\n').filter(line => line.includes(bondDetail));
assert(bond.length === 1);
return getStartEndCoords(bond[0]);
}
const angleDegBetweenVectors = (v1, v2) => 180 / Math.PI * Math.acos((v1[0] * v2[0] + v1[1] * v2[1])
/ Math.sqrt((v1[0] * v1[0] + v1[1] * v1[1]) * (v2[0] * v2[0] + v2[1] * v2[1])));
// the goal here isn't to be comprehensive (the RDKit has tests for that),
// just to make sure that the wrappers are working as expected
function test_basics() {
var bmol = null;
try {
bmol = RDKitModule.get_mol("c1ccccc");
assert(bmol === null);
} catch {
assert(bmol === null);
}
var mol = RDKitModule.get_mol("c1ccccc1O");
assert(mol !== null);
assert.equal(mol.get_smiles(),"Oc1ccccc1");
if (typeof Object.getPrototypeOf(mol).get_inchi === 'function') {
assert.equal(mol.get_inchi(),"InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H");
assert.equal(mol.get_inchi("-FixedH"),"InChI=1/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H");
}
if (typeof RDKitModule.get_inchikey_for_inchi === 'function') {
assert.equal(RDKitModule.get_inchikey_for_inchi(mol.get_inchi("-FixedH")),"ISWSIDIOOBJBQZ-UHFFFAOYNA-N");
assert.equal(RDKitModule.get_inchikey_for_inchi(mol.get_inchi()),"ISWSIDIOOBJBQZ-UHFFFAOYSA-N");
}
var mb = mol.get_molblock();
assert(mb.search("M END")>0);
var mol2 = RDKitModule.get_mol(mb);
assert(mol2 !== null);
assert.equal(mol2.get_smiles(),"Oc1ccccc1");
var mjson = mol.get_json();
assert(mjson.search("rdkitjson")>0);
var mol3 = RDKitModule.get_mol(mjson);
assert(mol3 !== null);
assert.equal(mol3.get_smiles(),"Oc1ccccc1");
var descrs = JSON.parse(mol.get_descriptors());
assert.equal(descrs.NumAromaticRings,1);
assert.equal(descrs.NumRings,1);
assert.equal(descrs.amw,94.11299);
var checkStringBinaryFpIdentity = (stringFp, binaryFp) => {
assert.equal(binaryFp.length, Math.ceil(stringFp.length / 8));
for (var i = 0, c = 0; i < binaryFp.length; ++i) {
var byte = 0;
for (var j = 0; j < 8; ++j, ++c) {
if (stringFp[c] === "1") {
byte |= (1 << j);
}
}
assert.equal(byte, binaryFp[i]);
}
};
{
var fp1 = mol.get_morgan_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 11);
var fp1Uint8Array = mol.get_morgan_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_morgan_fp(JSON.stringify({ radius: 0, nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 3);
var fp2Uint8Array = mol.get_morgan_fp_as_uint8array(JSON.stringify({ radius: 0, nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
{
var fp1 = mol.get_pattern_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 73);
var fp1Uint8Array = mol.get_pattern_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_pattern_fp(JSON.stringify({ nBits: 256 }));
assert.equal(fp2.length, 256);
assert.equal((fp2.match(/1/g)||[]).length, 65);
var fp2Uint8Array = mol.get_pattern_fp_as_uint8array(JSON.stringify({ nBits: 256 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
{
var fp1 = mol.get_topological_torsion_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 8);
var fp1Uint8Array = mol.get_topological_torsion_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_topological_torsion_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 8);
var fp2Uint8Array = mol.get_topological_torsion_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
{
var fp1 = mol.get_rdkit_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 38);
var fp1Uint8Array = mol.get_rdkit_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 37);
var fp2Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512, minPath: 2 }));
assert.equal(fp3.length, 512);
assert.equal((fp3.match(/1/g)||[]).length, 34);
var fp3Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512, minPath: 2 }));
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
var fp4 = mol.get_rdkit_fp(JSON.stringify({ nBits: 512, minPath: 2, maxPath: 4 }));
assert.equal(fp4.length, 512);
assert.equal((fp4.match(/1/g)||[]).length, 16);
var fp4Uint8Array = mol.get_rdkit_fp_as_uint8array(JSON.stringify({ nBits: 512, minPath: 2, maxPath: 4 }));
checkStringBinaryFpIdentity(fp4, fp4Uint8Array);
}
{
var fp1 = mol.get_atom_pair_fp();
assert.equal(fp1.length, 2048);
assert.equal((fp1.match(/1/g)||[]).length, 19);
var fp1Uint8Array = mol.get_atom_pair_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512 }));
assert.equal(fp2.length, 512);
assert.equal((fp2.match(/1/g)||[]).length, 19);
var fp2Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
var fp3 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512, minLength: 2 }));
assert.equal(fp3.length, 512);
assert.equal((fp3.match(/1/g)||[]).length, 13);
var fp3Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512, minLength: 2 }));
checkStringBinaryFpIdentity(fp3, fp3Uint8Array);
var fp4 = mol.get_atom_pair_fp(JSON.stringify({ nBits: 512, minLength: 2, maxLength: 3 }));
assert.equal(fp4.length, 512);
assert.equal((fp4.match(/1/g)||[]).length, 12);
var fp4Uint8Array = mol.get_atom_pair_fp_as_uint8array(JSON.stringify({ nBits: 512, minLength: 2, maxLength: 3 }));
checkStringBinaryFpIdentity(fp4, fp4Uint8Array);
}
{
var fp1 = mol.get_maccs_fp();
assert.equal(fp1.length, 167);
assert.equal((fp1.match(/1/g)||[]).length, 10);
var fp1Uint8Array = mol.get_maccs_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
}
if (typeof Object.getPrototypeOf(mol).get_avalon_fp === 'function') {
var fp1 = mol.get_avalon_fp();
assert.equal(fp1.length, 512);
assert.equal((fp1.match(/1/g)||[]).length, 19);
var fp1Uint8Array = mol.get_avalon_fp_as_uint8array();
checkStringBinaryFpIdentity(fp1, fp1Uint8Array);
var fp2 = mol.get_avalon_fp(JSON.stringify({ nBits: 2048 }));
assert.equal(fp2.length, 2048);
assert.equal((fp2.match(/1/g)||[]).length, 20);
var fp2Uint8Array = mol.get_avalon_fp_as_uint8array(JSON.stringify({ nBits: 2048 }));
checkStringBinaryFpIdentity(fp2, fp2Uint8Array);
}
var svg = mol.get_svg();
assert(svg.search("svg")>0);
var qmol = RDKitModule.get_qmol("Oc(c)c");
assert(qmol !== null);
var match = mol.get_substruct_match(qmol);
var pmatch = JSON.parse(match);
assert.equal(pmatch.atoms.length,4);
assert.equal(pmatch.atoms[0],6);
var svg2 = mol.get_svg_with_highlights(match);
assert(svg2.search("svg")>0);
assert(svg.search("#FF7F7F")<0);
assert(svg2.search("#FF7F7F")>0);
}
function test_molblock_nostrict() {
var molblock = `
MJ201100
10 10 0 0 0 0 0 0 0 0999 V2000
-1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 8 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
M STY 1 1 SUP
M SAL 1 4 7 8 9 10
M SMT 1 CF3
M SBL 1 1 7
M SAP 1 1 8
M END`;
var mol = RDKitModule.get_mol(molblock);
assert(mol !== null);
var mb = mol.get_molblock();
assert.equal(mb.includes("M SAP 1 1 8 6"), true);
var qmol = RDKitModule.get_qmol(molblock);
assert(qmol !== null);
var qmb = qmol.get_molblock();
assert.equal(qmb.includes("M SAP 1 1 8 6"), true);
}
function test_molblock_rgp() {
var molblock = `
MJ190400
9 9 0 0 0 0 0 0 0 0999 V2000
-6.5623 0.3105 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.1019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 0.3105 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.1019 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.9269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 -1.3394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.9269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7043 -1.3394 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.9898 -0.9268 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 7 4 0 0 0 0
2 3 4 0 0 0 0
2 7 4 0 0 0 0
5 8 1 0 0 0 0
8 9 1 0 0 0 0
1 2 1 0 0 0 0
M RGP 2 1 2 9 1
M END`;
var mol = RDKitModule.get_mol(molblock);
assert(mol !== null);
}
function test_get_aromatic_kekule_form() {
const aromRegExp = / \d \d 4 \d\n/g;
const kekRegExp = / \d \d [12] \d\n/g;
var mol = RDKitModule.get_mol("c1ccccc1");
var molblock = mol.get_molblock();
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
var molblock = mol.get_kekule_form();
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
molblock = mol.get_aromatic_form();
assert (molblock.match(aromRegExp).length === 6);
assert (molblock.match(kekRegExp) === null);
mol.delete();
mol = RDKitModule.get_qmol(`
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-0.6473 0.8696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3617 0.4571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3617 -0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6473 -0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0671 -0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0671 0.4571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 1 4 0 0 0 0
M END
`);
molblock = mol.get_aromatic_form();
assert (molblock.match(aromRegExp).length === 6);
assert (molblock.match(kekRegExp) === null);
molblock = mol.get_kekule_form();
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
mol.delete();
mol = RDKitModule.get_qmol(`
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-0.6473 0.8696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3617 0.4571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3617 -0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6473 -0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0671 -0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0671 0.4571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
M END
`);
molblock = mol.get_molblock(JSON.stringify({ kekulize: false }));
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
mol.convert_to_aromatic_form();
molblock = mol.get_molblock(JSON.stringify({ kekulize: false }));
assert (molblock.match(aromRegExp).length === 6);
assert (molblock.match(kekRegExp) === null);
mol.convert_to_kekule_form();
molblock = mol.get_molblock(JSON.stringify({ kekulize: false }));
assert (molblock.match(aromRegExp) === null);
assert (molblock.match(kekRegExp).length === 6);
mol.delete();
}
function test_sketcher_services() {
var mol = RDKitModule.get_mol("C[C@](F)(Cl)/C=C/C(F)Br");
assert(mol !== null);
var tags = mol.get_stereo_tags();
assert.equal(tags,'{"CIP_atoms":[[1,"(S)"],[6,"(?)"]],"CIP_bonds":[[4,5,"(E)"]]}');
}
function test_sketcher_services2() {
var mol = RDKitModule.get_mol("c1ccccc1");
assert(mol !== null);
var molb = mol.add_hs();
assert(molb.search(" H ")>0);
assert.equal((molb.match(/ H /g) || []).length,6);
var mol2 = RDKitModule.get_mol(molb);
assert(mol2 !== null);
var molb2 = mol2.get_molblock();
assert(molb2.search(" H ")>0);
assert.equal((molb2.match(/ H /g) || []).length,6);
molb2 = mol2.remove_hs();
assert(molb2.search(" H ")<0);
}
function test_abbreviations() {
var bmol = RDKitModule.get_mol("C1CC(C(F)(F)F)C1");
assert(bmol !== null);
var mapping = bmol.condense_abbreviations();
assert.equal(mapping, JSON.stringify({
atoms: [0, 1, 2, 3, 4, 5, 6, 7],
bonds: [0, 1, 2, 3, 4, 5, 6, 7],
}));
assert.equal(bmol.get_cxsmiles(),"FC(F)(F)C1CCC1");
mapping = bmol.condense_abbreviations(1.0,false);
assert.equal(mapping, JSON.stringify({
atoms: [0, 1, 2, 3, 7],
bonds: [0, 1, 2, 6, 7],
}));
assert.equal(bmol.get_cxsmiles(),"*C1CCC1 |$CF3;;;;$|");
}
function test_substruct_library(done) {
done.test_substruct_library = false;
var query = RDKitModule.get_qmol('C1CCCCN1');
var nonExistingQuery = RDKitModule.get_mol('O=C(O)C(c1ccc(cc1)CCN4CCC(c2nc3ccccc3n2CCOCC)CC4)(C)C');
const numBitOptions = [-1, 0];
var patternFpArray = [];
numBitOptions.forEach((numBits, optIdx) => {
var smiReader = readline.createInterface({
input: fs.createReadStream(__dirname + '/../../GraphMol/test_data/compounds.smi')
});
var sslib = numBits < 0 ? new RDKitModule.SubstructLibrary() : new RDKitModule.SubstructLibrary(numBits);
assert.equal(sslib.count_matches(query), 0);
assert.equal(sslib.get_matches(query), JSON.stringify([]));
assert.equal(sslib.get_matches_as_uint32array(query).length, 0);
// var t0 = performance.now()
// console.log('Started adding trusted SMILES');
var matches = [];
var expectedMatches = [39, 64, 80, 127, 128, 234, 240];
var i = 0;
var trustedSmiArray = []
smiReader.on('line', (smi) => {
sslib.add_trusted_smiles(smi);
var mol = RDKitModule.get_mol(smi);
var res = JSON.parse(mol.get_substruct_match(query));
if (res.atoms) {
matches.push(i);
}
++i;
mol.delete();
});
smiReader.on('close', () => {
// var t1 = performance.now();
// console.log('Finished adding trusted SMILES took ' + (t1 - t0) / 1000 + ' seconds');
for (var i = 0; i < sslib.size(); ++i) {
trustedSmiArray.push(sslib.get_trusted_smiles(i));
let excRaised = false;
try {
var fp = sslib.get_pattern_fp_as_uint8array(i);
patternFpArray.push(fp);
} catch (e) {
// this is expected to fail when numBits === 0
excRaised = true;
}
assert((excRaised && numBits === 0) || (!excRaised && numBits !== 0));
}
assert.equal(trustedSmiArray.length, sslib.size());
assert.equal(patternFpArray.length, sslib.size());
assert.equal(trustedSmiArray.length, patternFpArray.length);
var sslib2 = new RDKitModule.SubstructLibrary();
for (var i = 0; i < sslib.size(); ++i) {
sslib2.add_trusted_smiles_and_pattern_fp(trustedSmiArray[i], patternFpArray[i]);
}
assert.equal(sslib.size(), sslib2.size());
{
assert.equal(sslib.count_matches(query, false), 7);
var sslibMatches = sslib.get_matches(query);
assert.equal(sslibMatches, JSON.stringify(expectedMatches));
assert.equal(sslibMatches, JSON.stringify(matches));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(query);
assert.equal(sslibMatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslibMatchesUInt32Array[i], expectedMatches[i]);
}
}
{
assert.equal(sslib.count_matches(nonExistingQuery, false), 0);
var sslibMatches = sslib.get_matches(nonExistingQuery);
assert.equal(sslibMatches, JSON.stringify([]));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslibMatchesUInt32Array.length, 0);
}
{
assert.equal(sslib2.count_matches(query, false), 7);
var sslib2Matches = sslib2.get_matches(query);
assert.equal(sslib2Matches, JSON.stringify(expectedMatches));
assert.equal(sslib2Matches, JSON.stringify(matches));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(query);
assert.equal(sslib2MatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslib2MatchesUInt32Array[i], expectedMatches[i]);
}
}
{
assert.equal(sslib2.count_matches(nonExistingQuery, false), 0);
var sslib2Matches = sslib2.get_matches(nonExistingQuery);
assert.equal(sslib2Matches, JSON.stringify([]));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslib2MatchesUInt32Array.length, 0);
}
sslib.delete();
sslib2.delete();
if (optIdx === numBitOptions.length - 1) {
done.test_substruct_library = true;
query.delete();
nonExistingQuery.delete();
}
});
});
}
function test_substruct_library_merge_hs() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("c1ccccc1");
var mol2 = RDKitModule.get_mol("Cc1ccccc1");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol(`
MJ201100 2D
6 6 0 0 0 0 0 0 0 0999 V2000
-1.0491 0.7134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
5 6 2 0 0 0 0
1 2 2 0 0 0 0
6 1 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
M END`);
assert.equal(sslib.get_matches(query), JSON.stringify([0, 1]));
var query_hs = RDKitModule.get_mol(query.add_hs());
assert.equal(sslib.get_matches(query_hs), JSON.stringify([]));
query_hs = RDKitModule.get_mol(query_hs.get_molblock(), JSON.stringify({ mergeQueryHs: true }));
assert.equal(sslib.get_matches(query_hs), JSON.stringify([0]));
}
function test_substruct_library_empty_mols() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("");
var mol2 = RDKitModule.get_mol("");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol("C");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
var empty_query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(empty_query), JSON.stringify([]));
}
function test_substruct_library_empty_query() {
var sslib = new RDKitModule.SubstructLibrary();
var mol1 = RDKitModule.get_mol("C");
var mol2 = RDKitModule.get_mol("CC");
sslib.add_trusted_smiles(mol1.get_smiles());
sslib.add_trusted_smiles(mol2.get_smiles());
var query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
}
function test_substruct_library_empty_lib() {
var sslib = new RDKitModule.SubstructLibrary();
var query = RDKitModule.get_mol("C");
assert.equal(sslib.get_matches(query), JSON.stringify([]));
var empty_query = RDKitModule.get_mol("");
assert.equal(sslib.get_matches(empty_query), JSON.stringify([]));
}
function test_generate_aligned_coords() {
var smiles = "CCC";
var mol = RDKitModule.get_mol(smiles);
var template = "CC";
var qmol = RDKitModule.get_mol(template);
assert.equal(mol.generate_aligned_coords(qmol, JSON.stringify({useCoordGen: true})), "");
}
function test_isotope_labels() {
var mol = RDKitModule.get_mol("[1*]c1cc([2*])c([3*])c[14c]1");
assert(mol !== null);
var textIsoDummyIso = mol.get_svg_with_highlights(JSON.stringify({}));
var nLinesIsoDummyIso = textIsoDummyIso.split("\n").length;
var textNoIsoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ isotopeLabels: false }));
var nLinesNoIsoDummyIso = textNoIsoDummyIso.split("\n").length;
var textIsoNoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ dummyIsotopeLabels: false }));
var nLinesIsoNoDummyIso = textIsoNoDummyIso.split("\n").length;
var textNoIsoNoDummyIso = mol.get_svg_with_highlights(JSON.stringify({ isotopeLabels: false, dummyIsotopeLabels: false }));
var nLinesNoIsoNoDummyIso = textNoIsoNoDummyIso.split("\n").length;
var res = [nLinesNoIsoNoDummyIso, nLinesIsoNoDummyIso, nLinesNoIsoDummyIso, nLinesIsoDummyIso];
var resSorted = [...res];
resSorted.sort((a, b) => (a - b));
assert.ok(res.every((resItem, i) => (resItem === resSorted[i])));
}
function test_generate_aligned_coords_allow_rgroups() {
var template_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M RGP 3 7 1 8 2 9 3
M END`;
var ortho_meta_smiles = 'c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1';
var ortho_smiles = 'c1ccc(-c2ccccc2-c2ccccc2)cc1';
var meta_smiles = 'c1ccc(-c2cccc(-c3ccccc3)c2)cc1';
var para_smiles = 'c1ccc(-c2ccc(-c3ccccc3)cc2)cc1';
var biphenyl_smiles = 'c1ccccc1-c1ccccc1';
var phenyl_smiles = 'c1ccccc1';
var template_ref = RDKitModule.get_mol(template_molblock);
var ortho_meta = RDKitModule.get_mol(ortho_meta_smiles);
var ortho = RDKitModule.get_mol(ortho_smiles);
var meta = RDKitModule.get_mol(meta_smiles);
var para = RDKitModule.get_mol(para_smiles);
var biphenyl = RDKitModule.get_mol(biphenyl_smiles);
var phenyl = RDKitModule.get_mol(phenyl_smiles);
assert.equal(JSON.parse(ortho_meta.generate_aligned_coords(
template_ref, JSON.stringify({ useCoordGen: false, allowRGroups: true}))).atoms.length, 9);
[ true, false ].forEach(alignOnly => {
var opts = JSON.stringify({ useCoordGen: false, allowRGroups: true, alignOnly });
assert.equal(JSON.parse(ortho_meta.generate_aligned_coords(
template_ref, opts)).atoms.length, 9);
assert.equal(JSON.parse(ortho.generate_aligned_coords(
template_ref, opts)).atoms.length, 8);
assert.equal(JSON.parse(meta.generate_aligned_coords(
template_ref, opts)).atoms.length, 8);
assert.equal(JSON.parse(para.generate_aligned_coords(
template_ref, opts)).atoms.length, 8);
assert.equal(JSON.parse(biphenyl.generate_aligned_coords(
template_ref, opts)).atoms.length, 7);
assert.equal(JSON.parse(phenyl.generate_aligned_coords(
template_ref, opts)).atoms.length, 6);
});
const pyridineRef = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7144 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7144 -0.4124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7144 -0.4124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7144 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 7 1 0 0 0 0
4 8 1 0 0 0 0
M END
`);
const referenceSmarts = "[*:3]a1a([*:1])aa([*:2])aa1";
[ true, false ].forEach(alignOnly => {
var opts = JSON.stringify({ useCoordGen: false, allowRGroups: true, alignOnly, referenceSmarts });
assert.equal(JSON.parse(ortho_meta.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 8);
assert.equal(JSON.parse(ortho.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 7);
assert.equal(JSON.parse(meta.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 7);
assert.equal(JSON.parse(para.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 8);
assert.equal(JSON.parse(biphenyl.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 7);
assert.equal(JSON.parse(phenyl.generate_aligned_coords(
pyridineRef, opts)).atoms.length, 6);
});
}
function test_generate_aligned_coords_accept_failure() {
var template_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M RGP 3 7 1 8 2 9 3
M END
`;
var mol_molblock = `
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M END
`;
var template_ref = RDKitModule.get_mol(template_molblock);
var mol = RDKitModule.get_mol(mol_molblock);
var res = mol.generate_aligned_coords(template_ref, JSON.stringify({
useCoordGen: false,
allowRGroups: true,
acceptFailure: false
}));
assert(res === "");
assert.equal(mol.get_molblock(), mol_molblock);
res = mol.generate_aligned_coords(template_ref, JSON.stringify({
useCoordGen: false,
allowRGroups: true,
acceptFailure: true,
}));
assert(res === "{}");
assert.notEqual(mol.get_molblock(), mol_molblock);
var molNoCoords = RDKitModule.get_mol(mol.get_smiles());
assert(!molNoCoords.has_coords());
res = molNoCoords.generate_aligned_coords(template_ref, JSON.stringify({
useCoordGen: false,
allowRGroups: true,
acceptFailure: false,
}));
assert(res === "");
assert(!molNoCoords.has_coords());
res = molNoCoords.generate_aligned_coords(template_ref, JSON.stringify({
useCoordGen: false,
allowRGroups: true,
acceptFailure: true,
}));
assert(res === "{}");
assert(molNoCoords.has_coords());
}
function test_generate_aligned_coords_align_only() {
const template_molblock = `
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
-13.7477 6.3036 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-13.7477 4.7567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.6540 3.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.7477 2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.8414 3.6628 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-11.1071 3.6628 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
2 5 1 0
3 6 1 0
M RGP 2 1 1 6 2
M END
`;
const mol_molblock = `
RDKit 2D
18 22 0 0 0 0 0 0 0 0999 V2000
4.3922 -1.5699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9211 -2.0479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5995 -0.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3731 0.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8441 1.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0704 -0.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8666 0.7748 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7736 -0.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7749 -1.8666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7718 -1.8679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7731 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8679 0.7718 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.0718 -0.0598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3933 -1.5729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9222 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6008 -0.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3744 0.8016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8454 1.2795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9 10 1 0
11 10 1 0
11 8 1 0
8 9 1 0
4 5 1 0
6 5 1 0
7 6 1 0
3 4 1 0
3 7 1 0
1 6 1 0
2 3 1 0
2 1 1 0
17 18 1 0
13 18 1 0
12 13 1 0
16 17 1 0
16 12 1 0
14 13 1 0
15 16 1 0
15 14 1 0
12 11 1 0
8 7 1 0
M END
`;
const getCoordArray = (mol) => {
const molblock = mol.get_molblock().split("\n");
const numHeavyAtoms = parseInt(molblock[3].substr(0, 3));
return molblock.filter((_, idx) => idx > 3 && idx < 4 + numHeavyAtoms).map(
line => [0, 1, 2].map(i => parseFloat(line.substr(i * 10, (i + 1) * 10)))
);
};
const arraySum = (a) => {
const s = 0.;
return a.reduce((prev, curr) => prev + curr, s);
};
const sqDist = (xyz1, xyz2) => arraySum(xyz1.map((c, i) => (c - xyz2[i]) * (c - xyz2[i])))
const template_ref = RDKitModule.get_mol(template_molblock);
const mol = RDKitModule.get_mol(mol_molblock);
const molCoords = getCoordArray(mol);
const bondLength11_12 = Math.sqrt(sqDist(molCoords[11], molCoords[12]));
const bondLength5_6 = Math.sqrt(sqDist(molCoords[5], molCoords[6]));
assert(Math.abs(bondLength11_12 - bondLength5_6) < 1.e-4);
assert(bondLength11_12 > 2.3);
[ false, true ].forEach(alignOnly => {
const mol = RDKitModule.get_mol(mol_molblock);
const res = JSON.parse(mol.generate_aligned_coords(template_ref, JSON.stringify({ allowRGroups: true, alignOnly })));
assert([ 11, 10, 7, 8, 9, 6 ].every((idx, i) => res.atoms[i] === idx));
assert(mol.get_smiles() === "C1CC2CCC1N2C1CNC1N1C2CCC1CC2");
const molAliCoords = getCoordArray(mol);
const templateCoords = getCoordArray(template_ref);
res.atoms.forEach((molIdx, templateIdx) => {
assert(sqDist(molAliCoords[molIdx], templateCoords[templateIdx]) < 1.e-4);
});
const bondLengthAli11_12 = Math.sqrt(sqDist(molAliCoords[11], molAliCoords[12]));
const bondLengthAli5_6 = Math.sqrt(sqDist(molAliCoords[5], molAliCoords[6]));
assert(Math.abs(bondLengthAli11_12 - bondLengthAli5_6) < 1.e-4);
if (alignOnly) {
assert(bondLengthAli11_12 > 2.3);
} else {
assert(bondLengthAli11_12 < 1.6);
}
});
}
function test_get_mol_no_kekulize() {
var molIsValid = true;
try {
mol = RDKitModule.get_mol("c");
molIsValid = (mol !== null);
} catch (e) {
molIsValid = false;
}
assert(!molIsValid);
mol = RDKitModule.get_mol("c", JSON.stringify({kekulize: false}));
assert(mol !== null);
}
function test_get_smarts() {
var mol = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0491 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 -0.0661 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 2 0
5 8 1 0 0 2 0
M RGP 2 7 1 8 2
M END
`);
assert(mol !== null);
smarts = mol.get_smarts();
assert(smarts == "[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1-&!@*)-&!@*");
}
function test_get_cxsmarts() {
var mol = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0491 1.5839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 1.1714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 1.5839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
0.3798 -0.0661 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 2 0
5 8 1 0 0 2 0
M RGP 2 7 1 8 2
M END
`);
assert(mol !== null);
cxsmarts = mol.get_cxsmarts();
assert(cxsmarts == "[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1-&!@*)-&!@* |" +
"(-1.0491,1.5839,;-1.7635,1.1714,;-1.7635,0.3463,;-1.0491,-0.0661,;" +
"-0.3346,0.3463,;-0.3346,1.1714,;0.3798,1.5839,;0.3798,-0.0661,)," +
"atomProp:6.dummyLabel.R1:7.dummyLabel.R2|");
}
function test_normalize_depiction() {
var mol = RDKitModule.get_mol(`
MJ201100
9 10 0 0 0 0 0 0 0 0999 V2000
-1.5402 1.3161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2546 0.9036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2546 0.0785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5402 -0.3339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8257 0.0785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8257 0.9036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0411 -0.1764 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4438 0.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0410 1.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
8 9 2 0 0 0 0
6 9 1 0 0 0 0
7 8 1 0 0 0 0
5 7 1 0 0 0 0
M END
`);
const scalingFactor = mol.normalize_depiction();
assert(scalingFactor > 1.8 && scalingFactor < 1.9);
}
function test_straighten_depiction() {
var benzeneHoriz = RDKitModule.get_mol(`
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-0.0785 1.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9035 1.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3160 0.8928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9036 0.1783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0786 0.1783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3339 0.8929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
M END
`);
var benzeneVert = RDKitModule.get_mol(`
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
0.2234 1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4910 1.7178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2055 1.3053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2056 0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4911 0.0678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2234 0.4804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
M END
`);
var benzeneHorizCopy = RDKitModule.get_mol_copy(benzeneHoriz);
var benzeneVertCopy = RDKitModule.get_mol_copy(benzeneVert);
benzeneHoriz.straighten_depiction();
benzeneVert.straighten_depiction();
assert(benzeneHoriz.get_molblock() !== benzeneHorizCopy.get_molblock());
assert(benzeneVert.get_molblock() === benzeneVertCopy.get_molblock());
benzeneHoriz = benzeneHorizCopy;
benzeneVert = benzeneVertCopy;
benzeneHorizCopy = RDKitModule.get_mol_copy(benzeneHoriz);
benzeneVertCopy = RDKitModule.get_mol_copy(benzeneVert);
benzeneHoriz.straighten_depiction(true);
benzeneVert.straighten_depiction(true);
assert(benzeneHoriz.get_molblock() === benzeneHorizCopy.get_molblock());
assert(benzeneVert.get_molblock() === benzeneVertCopy.get_molblock());
}
function test_has_coords() {
var mol = RDKitModule.get_mol('CC');
assert(!mol.has_coords());
var mol2 = RDKitModule.get_mol(mol.get_new_coords());
assert(mol2.has_coords() === 2);
assert(!mol.has_coords());
mol.set_new_coords();
assert(mol.has_coords() === 2);
var mol3 = RDKitModule.get_mol(`
RDKit 3D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.5909 -0.6086 0.0018 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2459 0.8185 -0.0936 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8271 -0.1760 0.1017 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1425 -0.9648 0.9113 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8767 -1.2011 -0.8967 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5849 1.4596 0.7584 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2393 1.3618 -1.0674 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4853 -0.4161 -0.7761 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3678 -0.2732 1.0608 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 1 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
3 8 1 0
3 9 1 0
M END
`);
assert(mol3.has_coords() === 3);
}
function test_kekulize() {
const badAromaticSmiles = 'c1cccc1';
var mol = null;
try {
mol = RDKitModule.get_mol(badAromaticSmiles);
assert(mol === null);
} catch {
assert(mol === null);
}
mol = RDKitModule.get_mol(badAromaticSmiles, JSON.stringify({ kekulize: false }));
assert(mol !== null);
}
function test_sanitize() {
const badValenceSmiles = 'N(C)(C)(C)C';
var mol = null;
try {
mol = RDKitModule.get_mol(badValenceSmiles);
assert(mol === null);
} catch {
assert(mol === null);
}
try {
mol = RDKitModule.get_mol(badValenceSmiles, JSON.stringify({ kekulize: false }));
assert(mol === null);
} catch {
assert(mol === null);
}
mol = RDKitModule.get_mol(badValenceSmiles, JSON.stringify({ sanitize: false }));
assert(mol !== null);
}
function test_removehs() {
const badValenceSmiles = 'N1C=CC(=O)c2ccc(N(C)(C)(C)(C)C)cc12';
mol = RDKitModule.get_mol(badValenceSmiles, JSON.stringify({ sanitize: false, removeHs: false }));
assert(mol !== null);
}
function test_flexicanvas() {
var mol = RDKitModule.get_mol("CCCC");
assert(mol !== null);
var svg = mol.get_svg(-1,-1);
assert(svg.search("svg")>0);
assert(svg.search("width='87px'")>0);
assert(svg.search("height='19px'")>0);
}
function test_run_reaction() {
let rxn1;
let molList;
try {
rxn1 = RDKitModule.get_rxn('[#6:1][O:2]>>[#6:1]=[O:2]');
molList = molListFromSmiArray(['CC(C)O',]);
let products;
try {
products = rxn1.run_reactants(molList, 10000);
for (let i = 0; i < products.size(); i++) {
let element;
try {
element = products.get(i);
let mol;
try {
mol = element.next();
assert(mol && mol.get_smiles() === "CC(C)=O");
} finally {
if (mol) {
mol.delete();
}
}
} finally {
if (element) {
element.delete();
}
}
}
} finally {
if (products) {
products.delete();
}
}
} finally {
if (rxn1) {
rxn1.delete();
}
if (molList) {
molList.delete();
}
}
}
function test_rxn_drawing() {
{
var rxn = RDKitModule.get_rxn("[CH3:1][OH:2]>>[CH2:1]=[OH0:2]");
var svg = rxn.get_svg();
assert(svg.search("svg") > 0);
var rxn_from_block = RDKitModule.get_rxn(`$RXN
RDKit
1 1
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 6 0
V 1 [C&H3:1]
V 2 [O&H1:2]
M END
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 2 0
V 1 [C&H2:1]
V 2 [O&H0:2]
M END`);
var svg_from_block = rxn_from_block.get_svg();
assert(svg_from_block.search("svg") > 0);
assert(svg.match(/<path/g).length > 0);
assert(svg.match(/<path/g).length === svg_from_block.match(/<path/g).length);
}
{
var rxn = RDKitModule.get_rxn("[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-:15]",
JSON.stringify({ useSmiles: true }));
{
var svg = rxn.get_svg();
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({ kekulize: false }));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" > 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({ highlightByReactant: true }));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") > 0);
assert(svg.search("#BCD6ED") < 0);
assert(svg.search("#A8D08D") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({
highlightColorsReactants: [[.741, .843, .933], [.659, .816, .553]]
}));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") < 0);
}
{
var svg = rxn.get_svg_with_highlights(JSON.stringify({
highlightByReactant: true,
highlightColorsReactants: [[.741, .843, .933], [.659, .816, .553]]
}));
assert(svg.search("svg") > 0);
assert(svg.search("stroke-dasharray" < 0));
assert(svg.search("ellipse") > 0);
assert(svg.search("#BCD6ED") > 0);
assert(svg.search("#A8D08D") > 0);
}
rxn.delete();
}
{
var rxn = RDKitModule.get_rxn("[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-:15]");
var hasThrown = false;
var isAromatic = false;
// if the code is built with exception support it will not throw
// but rather display molecules in their aromatic form rather
// than kekulized
try {
var svg = rxn.get_svg();
isAromatic = svg.search("stroke-dasharray" > 0);
} catch {
hasThrown = true;
}
assert(isAromatic || hasThrown);
}
}
function test_legacy_stereochem() {
var origSetting;
try {
origSetting = RDKitModule.use_legacy_stereo_perception(true);
var mol = RDKitModule.get_mol("O[C@@]1(C)C/C(/C1)=C(/C)\\CC");
assert(mol !== null);
assert.equal(mol.get_smiles(),"CCC(C)=C1CC(C)(O)C1");
RDKitModule.use_legacy_stereo_perception(false);
mol = RDKitModule.get_mol("O[C@@]1(C)C/C(/C1)=C(/C)\\CC");
assert(mol !== null);
assert.equal(mol.get_smiles(),"CC/C(C)=C1\\C[C@](C)(O)C1");
} finally {
RDKitModule.use_legacy_stereo_perception(origSetting);
}
}
function test_allow_non_tetrahedral_chirality() {
var ctab = `
Mrv2108 09132105183D
5 4 0 0 0 0 999 V2000
-1.2500 1.4518 0.0000 Pt 0 0 0 0 0 0 0 0 0 0 0 0
-1.2500 2.2768 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.4250 1.4518 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-2.0750 1.4518 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-1.2500 0.6268 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
`;
var origSetting;
try {
origSetting = RDKitModule.allow_non_tetrahedral_chirality(true);
var mol = RDKitModule.get_mol(ctab);
assert(mol !== null);
assert.equal(mol.get_smiles(), "F[Pt@SP3](F)(Cl)Cl");
RDKitModule.allow_non_tetrahedral_chirality(false);
var mol = RDKitModule.get_mol(ctab);
assert(mol !== null);
assert.equal(mol.get_smiles(), "F[Pt](F)(Cl)Cl");
} finally {
RDKitModule.allow_non_tetrahedral_chirality(origSetting);
}
}
function test_prop() {
var mol = RDKitModule.get_mol(`
MJ201900
2 1 0 0 0 0 0 0 0 0999 V2000
0.1899 1.9526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5245 1.5401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M END
`);
assert.equal(mol.has_prop("test1"), false);
assert.equal(mol.set_prop("test1","val"), true);
assert.equal(mol.has_prop("test1"), true);
assert.equal(mol.get_prop("test1"),"val");
assert.equal(mol.set_prop("test2","val"), true);
props = mol.get_prop_list(false, false);
assert.equal(props.get(0), "test1");
assert.equal(props.get(1), "test2");
assert.equal(mol.clear_prop("test3"), false);
assert.equal(mol.has_prop("test2"), true);
assert.equal(mol.clear_prop("test2"), true);
assert.equal(mol.has_prop("test2"), false);
}
function test_highlights() {
var mol = RDKitModule.get_mol('c1cc(O)ccc1');
var svg = mol.get_svg_with_highlights(JSON.stringify({
highlightAtomColors: {
0: [1.0, 0.0, 0.0],
1: [1.0, 0.0, 0.0],
2: [1.0, 0.0, 0.0],
3: [0.0, 1.0, 0.0],
4: [1.0, 0.0, 0.0],
5: [1.0, 0.0, 0.0],
6: [1.0, 0.0, 0.0],
}, highlightBondColors: {
2: [0.0, 0.7, 0.9],
}, highlightAtomRadii: {
0: 0.1,
1: 0.1,
2: 0.1,
3: 0.8,
4: 0.1,
5: 0.1,
6: 0.1,
}, atoms: [0, 1, 2, 3, 4, 5, 6], bonds: [2], width: 127
}));
assert(!svg.includes('fill:#FF7F7F'));
assert(svg.includes('fill:#FF0000'));
assert(svg.includes('fill:#00FF00'));
assert(svg.includes('fill:#00B2E5'));
assert(svg.includes("width='127px'"));
assert(svg.includes('</svg>'));
}
function test_add_chiral_hs() {
var mol = RDKitModule.get_mol(`
MJ201100
18 21 0 0 1 0 0 0 0 0999 V2000
-0.8540 -1.4441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3019 -0.8310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5185 -0.9172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8540 -0.1635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6825 0.6434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1379 0.7296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5504 1.4441 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4734 -0.0239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2409 0.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6609 -1.2726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2130 -1.8857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9580 -2.6703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1511 -2.8419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5990 -2.2287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0201 -1.7143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5720 -2.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3171 -3.1121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5100 -3.2835 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
4 3 1 0 0 0 0
4 5 1 0 0 0 0
6 5 1 0 0 0 0
6 7 1 1 0 0 0
6 8 1 0 0 0 0
8 9 1 1 0 0 0
8 2 1 0 0 0 0
4 9 1 1 0 0 0
2 1 1 1 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
1 10 2 0 0 0 0
1 14 1 0 0 0 0
15 16 2 0 0 0 0
16 17 1 0 0 0 0
11 15 1 0 0 0 0
17 18 2 0 0 0 0
12 18 1 0 0 0 0
M END
`);
var quinoline_scaffold = RDKitModule.get_mol(`
MJ201100
10 11 0 0 1 0 0 0 0 0999 V2000
-8.1001 2.8219 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-8.8145 2.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.8145 1.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.1001 1.1718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3856 1.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3856 2.4094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.6711 1.1718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.9566 1.5842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.9566 2.4092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.6711 2.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
5 7 1 0 0 0 0
10 6 1 0 0 0 0
1 2 2 0 0 0 0
6 1 1 0 0 0 0
M END
`);
var svg1 = mol.get_svg_with_highlights(JSON.stringify({width: 350, height: 300}));
assert(svg1.includes("width='350px'"));
assert(svg1.includes("height='300px'"));
assert(svg1.includes("</svg>"));
assert(svg1.includes("atom-17"));
assert(svg1.includes("atom-18"));
assert(svg1.includes("atom-19"));
var svg2 = mol.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
assert(svg2.includes("width='350px'"));
assert(svg2.includes("height='300px'"));
assert(svg2.includes("</svg>"));
assert(svg2.includes("atom-17"));
assert(!svg2.includes("atom-18"));
assert(!svg2.includes("atom-19"));
assert(mol.get_molblock().includes("4 3 1 6"));
var molblock = mol.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(!molblock.includes("4 3 1 6"));
assert(molblock.includes("6 7 1 1"));
// Here we want to test that the original molblock wedging is preserved and inverted
// as the coordinates are rigid-body rotated
var molCopy;
molCopy = RDKitModule.get_mol_copy(mol);
assert(JSON.parse(molCopy.generate_aligned_coords(quinoline_scaffold, JSON.stringify({ acceptFailure: false, alignOnly: true }))));
molblock = molCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(molblock.split('\n').some(line => line.match(/^ [1 ]\d [1 ]\d [12] 6 *$/)));
assert(!molblock.split('\n').some(line => line.match(/^ [1 ]\d [1 ]\d [12] 1 *$/)));
assert(!molblock.includes("4 3 1 6"));
assert(molblock.includes("6 7 1 6"));
molCopy.delete();
// Here we want to test that the original molblock wedging gets cleared
// and hence wedging is recomputed as the coordinates are re-generated
molCopy = RDKitModule.get_mol_copy(mol);
assert(JSON.parse(molCopy.generate_aligned_coords(quinoline_scaffold, JSON.stringify({ acceptFailure: false }))));
molblock = molCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(molblock.split('\n').some(line => line.match(/^ [1 ]\d [1 ]\d [12] 6 *$/)));
assert(molblock.split('\n').some(line => line.match(/^ [1 ]\d [1 ]\d [12] 1 *$/)));
molCopy.delete();
mol.delete();
quinoline_scaffold.delete();
}
function getWedgedMolAndInvertedWedges() {
const wedgedMol = RDKitModule.get_mol(`
RDKit 2D
29 34 0 0 1 0 0 0 0 0999 V2000
1.3719 5.1304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.5985 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9482 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7216 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2685 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8994 3.5835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5597 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5597 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8994 6.6771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.2389 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.5784 6.6771 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-5.2389 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3719 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5985 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3719 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9188 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6921 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9188 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2389 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0124 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2389 -1.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6921 -1.5673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.8996 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2391 -4.2467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5777 -6.5331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9909 -5.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0124 -2.9070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3306 -6.6772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5784 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
3 4 1 0
5 4 1 6
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 1
5 9 1 0
9 10 1 0
10 11 1 1
10 12 1 0
6 12 1 1
2 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 17 1 0
17 18 2 0
13 18 1 0
17 19 1 0
19 20 1 0
20 21 1 0
21 22 1 0
16 22 1 0
23 24 1 0
23 25 1 0
25 26 1 0
24 27 1 0
27 26 1 0
26 28 1 0
24 29 1 0
28 29 1 0
21 27 1 0
M END
`);
const invertedWedges = ` 2 1 1 6
2 3 1 0
3 4 1 0
5 4 1 1
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 6
5 9 1 0
9 10 1 0
10 11 1 6
10 12 1 0
6 12 1 6
2 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 17 1 0
17 18 2 0
13 18 1 0
17 19 1 0
19 20 1 0
20 21 1 0
21 22 1 0
16 22 1 0
23 24 1 0
23 25 1 0
25 26 1 0
24 27 1 0
27 26 1 0
26 28 1 0
24 29 1 0
28 29 1 0
21 27 1 0
`;
return { wedgedMol, invertedWedges };
}
function test_wedging_all_within_scaffold() {
const { wedgedMol, invertedWedges } = getWedgedMolAndInvertedWedges();
const scaffold = RDKitModule.get_mol(`
RDKit 2D
13 14 0 0 1 0 0 0 0 0999 V2000
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2953 4.1222 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0
2 3 1 0
3 4 1 0
5 4 1 1
5 6 1 0
6 7 1 6
7 8 1 0
9 8 1 6
5 9 1 0
9 10 1 0
10 11 1 6
10 12 1 0
6 12 1 0
2 13 1 6
M END
`);
// the "alignOnly" alignment should succeed and preserve molblock wedging
// (inverted with respect to the original molecule)
// it should feature a narrow angle between the bridge bonds
// as the original geometry of the bridge is preserved
let wedgedMolCopy;
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false, alignOnly: true }))));
const mbAlignOnly = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgAlignOnly = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgAlignOnly, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgAlignOnly, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 10 && v1v2Theta < 15);
}
assert(mbAlignOnly.includes(invertedWedges));
// the "rebuild" alignment should succeed and preserve molblock wedging
// (inverted with respect to the original molecule)
// it should feature a much wider angle between the bridge bonds as the
// bridged system is entirely rebuilt since it is not part of the scaffold
wedgedMolCopy.delete();
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false }))));
const mbRebuild = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgRebuild = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgRebuild, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgRebuild, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 105 && v1v2Theta < 110);
}
assert(mbRebuild.includes(invertedWedges));
// the "rebuildCoordGen" alignment should succeed and clear original wedging
// it should feature an even wider angle between the bridge bonds as CoordGen
// has a template for the bridged system.
// Additionally, CoordGen also rebuilds the scaffold, therefore original wedging
// should be cleared
wedgedMolCopy.delete();
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false, useCoordGen: true }))));
const mbRebuildCoordGen = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgRebuildCoordGen = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgRebuildCoordGen, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgRebuildCoordGen, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 145 && v1v2Theta < 150);
}
assert(!mbRebuildCoordGen.includes(invertedWedges));
wedgedMolCopy.delete();
}
function test_wedging_outside_scaffold() {
const { wedgedMol, invertedWedges } = getWedgedMolAndInvertedWedges();
const scaffold = RDKitModule.get_mol(`
RDKit 2D
9 10 0 0 1 0 0 0 0 0999 V2000
-0.8816 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6651 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2958 -0.9804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0435 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0435 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2958 2.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6355 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9750 2.1129 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
2.6355 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
3 4 1 6
4 5 1 0
6 5 1 6
2 6 1 0
6 7 1 0
7 8 1 6
7 9 1 0
3 9 1 0
M END
`);
let wedgedMolCopy;
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
// the "alignOnly" alignment should succeed and preserve molblock wedging
// (inverted with respect to the original molecule)
// it should feature a narrow angle between the bridge bonds
// as the original geometry of the bridge is preserved
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false, alignOnly: true }))));
const mbAlignOnly = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgAlignOnly = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgAlignOnly, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgAlignOnly, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 10 && v1v2Theta < 15);
}
assert(mbAlignOnly.includes(invertedWedges));
// the "rebuild" alignment should succeed and clear original wedging
// it should feature a much wider angle between the bridge bonds as the
// bridged system is entirely rebuilt since it is not part of the scaffold
wedgedMolCopy.delete();
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false }))));
const mbRebuild = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgRebuild = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgRebuild, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgRebuild, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 105 && v1v2Theta < 110);
}
assert(!mbRebuild.includes(invertedWedges));
// the "rebuildCoordGen" alignment should succeed and clear original wedging
// it should feature an even wider angle between the bridge bonds as CoordGen
// has a template for the bridged system.
// Additionally, CoordGen also rebuilds the scaffold, therefore original wedging
// should be cleared
wedgedMolCopy.delete();
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(JSON.parse(wedgedMolCopy.generate_aligned_coords(scaffold, JSON.stringify({ acceptFailure: false, useCoordGen: true }))));
const mbRebuildCoordGen = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
const svgRebuildCoordGen = wedgedMolCopy.get_svg_with_highlights(JSON.stringify({
width: 350, height: 300, useMolBlockWedging: true, wedgeBonds: false, addChiralHs: false
}));
{
const [xy23, xy26] = extractBondCoords(svgRebuildCoordGen, 'atom-23 atom-26');
const [_, xy25] = extractBondCoords(svgRebuildCoordGen, 'atom-26 atom-25');
const v1 = [xy23[0] - xy26[0], xy23[1] - xy26[1]];
const v2 = [xy25[0] - xy26[0], xy25[1] - xy26[1]];
const v1v2Theta = angleDegBetweenVectors(v1, v2);
assert(v1v2Theta > 145 && v1v2Theta < 150);
}
assert(!mbRebuildCoordGen.includes(invertedWedges));
wedgedMolCopy.delete();
}
function test_wedging_if_no_match() {
const { wedgedMol, invertedWedges } = getWedgedMolAndInvertedWedges();
const scaffoldNoMatch = RDKitModule.get_mol(`
RDKit 2D
13 14 0 0 1 0 0 0 0 0999 V2000
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2953 4.1222 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0
2 3 1 0
3 4 1 0
5 4 1 1
5 6 1 0
6 7 1 6
7 8 1 0
9 8 1 6
5 9 1 0
9 10 1 0
10 11 1 6
10 12 1 0
6 12 1 0
2 13 1 6
M END
`);
let wedgedMolCopy;
let mb;
const origMolBlock = wedgedMol.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
// the "alignOnly" alignment should return "" if acceptFailure is false
// and preserve the original coordinates
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: false, alignOnly: true })) === "");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb === origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
// the "alignOnly" alignment should return "{}" if acceptFailure is true
// and generate new coordinates, hence wedging should be cleared
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: true, alignOnly: true })) === "{}");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb !== origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
// the "rebuild" alignment should return "" if acceptFailure is false
// and preserve the original coordinates
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: false })) === "");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb === origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
// the "rebuild" alignment should return "{}" if acceptFailure is true
// and generate new coordinates, hence wedging should be cleared
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: true })) === "{}");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb !== origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
// the "rebuildCoordGen" alignment should return "" if acceptFailure is false
// and preserve the original coordinates
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: false, useCoordGen: true })) === "");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb === origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
// the "rebuildCoordGen" alignment should return "{}" if acceptFailure is true
// and generate new coordinates, hence wedging should be cleared
wedgedMolCopy = RDKitModule.get_mol_copy(wedgedMol);
assert(wedgedMolCopy.generate_aligned_coords(scaffoldNoMatch, JSON.stringify({ acceptFailure: true, useCoordGen: true })) === "{}");
mb = wedgedMolCopy.get_molblock(JSON.stringify({ useMolBlockWedging: true }));
assert(mb !== origMolBlock);
assert(!mb.includes(invertedWedges));
wedgedMolCopy.delete();
}
function test_get_frags() {
{
var mol = RDKitModule.get_mol("n1ccccc1.CC(C)C.OCCCN");
var expectedFragSmiles = ["c1ccncc1", "CC(C)C", "NCCCO"];
var expectedFragSmilesNonSanitized = ["CN(C)(C)C", "c1ccc1"];
var expectedMappings = {
frags: [0,0,0,0,0,0,1,1,1,1,2,2,2,2,2],
fragsMolAtomMapping: [[0,1,2,3,4,5],[6,7,8,9],[10,11,12,13,14]],
};
var { molList, mappings } = mol.get_frags();
assert(molList.size() === 3);
assert(JSON.stringify(JSON.parse(mappings)) === JSON.stringify(expectedMappings));
var i = 0;
while (!molList.at_end()) {
var mol = molList.next();
assert(mol.get_smiles() === expectedFragSmiles[i++]);
mol.delete();
}
assert(!molList.next());
molList.delete();
}
{
var mol = RDKitModule.get_mol("N(C)(C)(C)C.c1ccc1", JSON.stringify({sanitize: false}));
var exceptionThrown = false;
try {
mol.get_frags();
} catch (e) {
exceptionThrown = true;
}
assert(exceptionThrown);
var { molList, mappings } = mol.get_frags(JSON.stringify({sanitizeFrags: false}));
assert(molList.size() === 2);
var i = 0;
while (!molList.at_end()) {
var mol = molList.next();
assert(mol.get_smiles() === expectedFragSmilesNonSanitized[i++]);
mol.delete();
}
assert(!molList.next());
molList.delete();
}
}
function test_get_mmpa_frags() {
{
var mol = RDKitModule.get_mol("CC(C)CCN1C(=O)CN=C(c2ccccc12)C3CCCCC3");
var expectedCores = ["O=C1CN=C(C2CCCCC2)c2ccccc2N1CCC([*:1])[*:2]", "CC([*:1])[*:2]", "CC(C[*:2])[*:1]", "CC(CC[*:2])[*:1]",
"CC(CCN1C(=O)CN=C([*:2])c2ccccc21)[*:1]", "C([*:1])[*:2]", "C(C[*:2])[*:1]", "O=C1CN=C([*:2])c2ccccc2N1CC[*:1]",
"C([*:1])[*:2]", "O=C1CN=C([*:1])c2ccccc2N1C[*:2]", "O=C1CN=C([*:1])c2ccccc2N1[*:2]"];
var expectedSidechains = ["C[*:1].C[*:2]", "C[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1CC[*:2]", "C[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1C[*:2]",
"C[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1[*:2]", "C1CCC([*:2])CC1.C[*:1]", "CC(C)[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1C[*:2]",
"CC(C)[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1[*:2]", "C1CCC([*:2])CC1.CC(C)[*:1]", "CC(C)C[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1[*:2]",
"C1CCC([*:1])CC1.CC(C)C[*:2]", "C1CCC([*:1])CC1.CC(C)CC[*:2]"];
var pairs = mol.get_mmpa_frags(2, 2, 20);
assert(pairs.cores);
assert(pairs.cores.size() === 11);
assert(pairs.sidechains);
assert(pairs.sidechains.size() === 11);
var i = 0;
while (!pairs.cores.at_end()) {
var m = pairs.cores.next();
assert(m.get_smiles() === expectedCores[i++]);
m.delete();
}
i = 0;
while (!pairs.sidechains.at_end()) {
var m = pairs.sidechains.next();
assert(m.get_smiles() === expectedSidechains[i++]);
m.delete();
}
assert(!pairs.cores.next());
assert(!pairs.sidechains.next());
pairs.cores.delete();
pairs.sidechains.delete();
mol.delete();
}
{
var mol = RDKitModule.get_mol("CC(C)CCN1C(=O)CN=C(c2ccccc12)C3CCCCC3");
var expectedSidechains = ["CC(CCN1C(=O)CN=C(C2CCCCC2)c2ccccc21)[*:1].C[*:1]",
"CC(C)[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1CC[*:1]", "CC(C)C[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1C[*:1]",
"CC(C)CC[*:1].O=C1CN=C(C2CCCCC2)c2ccccc2N1[*:1]", "C1CCC([*:1])CC1.CC(C)CCN1C(=O)CN=C([*:1])c2ccccc21"];
var pairs = mol.get_mmpa_frags(1, 1, 20);
assert(pairs.cores);
assert(pairs.cores.size() === 5);
assert(pairs.sidechains);
assert(pairs.sidechains.size() === 5);
while (!pairs.cores.at_end()) {
var m = pairs.cores.next();
assert(m === null);
}
var i = 0;
while (!pairs.sidechains.at_end()) {
var m = pairs.sidechains.next();
assert(m.get_smiles() === expectedSidechains[i++]);
m.delete();
}
assert(!pairs.cores.next());
assert(!pairs.sidechains.next());
var numCores = pairs.cores.size();
for (i = 0; i < numCores; ++i) {
assert(pairs.cores.at(i) === null);
}
for (i = 0; i < numCores; ++i) {
assert(pairs.cores.pop(0) === null);
}
assert(pairs.cores.size() === 0);
assert(pairs.cores.next() === null);
pairs.cores.delete();
pairs.sidechains.delete();
mol.delete();
}
}
function test_hs_in_place() {
{
var mol = RDKitModule.get_mol("CC");
assert(!mol.has_coords());
var descNoH = JSON.parse(mol.get_descriptors());
assert(`${descNoH.chi0v}` === '2');
assert(`${descNoH.chi1v}` === '1');
mol.add_hs_in_place();
assert(!mol.has_coords());
assert(mol.get_smiles() === '[H]C([H])([H])C([H])([H])[H]');
var descH = JSON.parse(mol.get_descriptors());
assert(`${descH.chi0v}` === '1');
assert(`${descH.chi1v}` === '0.25');
mol.delete();
}
{
var mol = RDKitModule.get_mol("C([H])([H])([H])C([H])([H])[H]", JSON.stringify({ removeHs: false }));
assert(!mol.has_coords());
var descH = JSON.parse(mol.get_descriptors());
assert(`${descH.chi0v}` === '1');
assert(`${descH.chi1v}` === '0.25');
mol.remove_hs_in_place();
assert(!mol.has_coords());
assert(mol.get_smiles() === 'CC');
var descNoH = JSON.parse(mol.get_descriptors());
assert(`${descNoH.chi0v}` === '2');
assert(`${descNoH.chi1v}` === '1');
mol.delete();
}
{
var mol = RDKitModule.get_mol(`
MJ201100
2 1 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
`);
assert(mol.has_coords());
assert(mol.get_molblock() === `
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
`);
var descNoH = JSON.parse(mol.get_descriptors());
assert(`${descNoH.chi0v}` === '2');
assert(`${descNoH.chi1v}` === '1');
mol.add_hs_in_place();
assert(mol.has_coords());
assert(mol.get_smiles() === '[H]C([H])([H])C([H])([H])[H]');
var descH = JSON.parse(mol.get_descriptors());
assert(`${descH.chi0v}` === '1');
assert(`${descH.chi1v}` === '0.25');
assert(mol.get_molblock().includes(`
RDKit 2D
8 7 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
`));
assert(mol.get_molblock().includes(` 1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
`));
mol.delete();
}
{
var mol = RDKitModule.get_mol(`
MJ201100
8 7 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.4080 5.8260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-14.7100 4.6991 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.5830 4.3971 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.8685 4.8096 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.5665 5.9366 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.6935 6.2385 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
2 6 1 0 0 0 0
2 7 1 0 0 0 0
2 8 1 0 0 0 0
M END
`, JSON.stringify({ removeHs: false }));
assert(mol.has_coords());
assert(mol.get_molblock() === `
RDKit 2D
8 7 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.4080 5.8260 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-14.7100 4.6991 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.5830 4.3971 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.8685 4.8096 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-12.5665 5.9366 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-13.6935 6.2385 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
`);
var descH = JSON.parse(mol.get_descriptors());
assert(`${descH.chi0v}` === '1');
assert(`${descH.chi1v}` === '0.25');
mol.remove_hs_in_place();
assert(mol.has_coords());
assert(mol.get_smiles() === 'CC');
var descNoH = JSON.parse(mol.get_descriptors());
assert(`${descNoH.chi0v}` === '2');
assert(`${descNoH.chi1v}` === '1');
assert(mol.get_molblock() === `
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
-13.9955 5.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.2810 5.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
`);
mol.delete();
}
}
function test_query_colour() {
var mol;
try {
mol = RDKitModule.get_qmol('c1ccc2nc([*:1])nc([*:2])c2c1');
var svg1 = mol.get_svg_with_highlights(JSON.stringify({width: 350, height: 300}));
assert(svg1.includes("width='350px'"));
assert(svg1.includes("height='300px'"));
assert(svg1.includes("</svg>"));
assert(svg1.includes("#7F7F7F"));
var svg2 = mol.get_svg_with_highlights(JSON.stringify({width: 350, height: 300, queryColour: [0.0, 0.0, 0.0]}));
assert(svg2.includes("width='350px'"));
assert(svg2.includes("height='300px'"));
assert(svg2.includes("</svg>"));
assert(!svg2.includes("#7F7F7F"));
} finally {
if (mol) {
mol.delete();
}
}
}
function test_alignment_r_groups_aromatic_ring() {
var mol;
var scaffold;
try {
mol = RDKitModule.get_mol('c1ccc2nccnc2c1');
assert(mol !== null);
scaffold = RDKitModule.get_mol(`
MJ201100
8 8 0 0 0 0 0 0 0 0999 V2000
-1.0263 -0.3133 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-2.4553 0.5116 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-1.7408 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7408 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4553 -1.9633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1698 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1698 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4553 -0.3133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 1 0 0 0 0
8 2 1 0 0 0 0
4 3 2 0 0 0 0
5 4 1 0 0 0 0
6 5 2 0 0 0 0
7 6 1 0 0 0 0
8 3 1 0 0 0 0
8 7 2 0 0 0 0
M RGP 2 1 2 2 1
M END`);
assert(scaffold !== null);
var res = mol.generate_aligned_coords(scaffold, JSON.stringify({useCoordGen: true, allowRGroups: true}));
assert(res);
assert.equal(JSON.parse(res).atoms.length, 8);
assert.equal(JSON.parse(res).bonds.length, 8);
} finally {
if (mol) {
mol.delete();
}
}
try {
mol = RDKitModule.get_mol(`
MJ201100
10 11 0 0 0 0 0 0 0 0999 V2000
3.6937 2.5671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8687 2.5671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4561 1.8526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8687 1.1382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6937 1.1381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1062 1.8526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9313 1.8527 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.3438 2.5671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9313 3.2816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1062 3.2816 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5 6 1 0 0 0 0
4 5 2 0 0 0 0
3 4 1 0 0 0 0
2 3 2 0 0 0 0
1 6 2 0 0 0 0
1 2 1 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 1 1 0 0 0 0
7 8 2 0 0 0 0
6 7 1 0 0 0 0
M END`);
var res = mol.generate_aligned_coords(scaffold, JSON.stringify({allowRGroups: true, alignOnly: true}));
assert(res);
assert.equal(JSON.parse(res).atoms.length, 8);
assert.equal(JSON.parse(res).bonds.length, 8);
} finally {
if (mol) {
mol.delete();
}
if (scaffold) {
scaffold.delete();
}
}
}
function test_is_valid_deprecated() {
var mol = RDKitModule.get_mol('C');
assert(mol !== null);
assert(mol.is_valid());
var mol;
try {
mol = RDKitModule.get_mol('CN(C)(C)C');
} catch (e) {
// in case MinimalLib was built without exception support
mol = null;
}
assert(mol === null);
if (RDKitModule.get_rxn) {
var rxn;
rxn = RDKitModule.get_rxn('C>>N');
assert(rxn !== null);
try {
rxn = RDKitModule.get_rxn('Z>>C');
} catch (e) {
// in case MinimalLib was built without exception support
rxn = null;
}
assert(rxn === null);
}
}
function molListFromSmiArray(smiArray) {
const molList = new RDKitModule.MolList();
assert(molList);
smiArray.forEach((smiName) => {
const [smi, name] = smiName.split(' ');
let mol;
try {
mol = RDKitModule.get_mol(smi);
assert(mol);
molList.append(mol);
} finally {
if (mol) {
mol.delete();
}
}
});
return molList;
}
function test_mol_list() {
const smiArray = [ 'C1CC1', 'C1CCCC1' ];
let molList;
let mol;
try {
molList = molListFromSmiArray(smiArray);
assert(molList);
assert.equal(molList.size(), 2);
assert(!molList.at_end());
try {
mol = molList.next();
assert(mol);
} finally {
if (mol) {
mol.delete();
}
}
try {
mol = molList.next();
assert(mol);
} finally {
if (mol) {
mol.delete();
}
}
mol = molList.next();
assert(!mol);
assert(molList.at_end());
try {
mol = molList.at(0);
assert.equal(mol.get_num_atoms(), 3);
} finally {
if (mol) {
mol.delete();
}
}
try {
mol = molList.at(1);
assert.equal(mol.get_num_atoms(), 5);
} finally {
if (mol) {
mol.delete();
}
}
assert(molList.at_end());
try {
mol = RDKitModule.get_mol('C1CCC1');
assert(mol);
molList.insert(1, mol);
assert.equal(molList.size(), 3);
assert(!molList.at_end());
} finally {
if (mol) {
mol.delete();
}
}
molList.reset();
assert(!molList.at_end());
try {
mol = molList.at(1);
assert.equal(mol.get_num_atoms(), 4);
} finally {
if (mol) {
mol.delete();
}
}
try {
mol = molList.pop(0);
assert.equal(mol.get_num_atoms(), 3);
} finally {
if (mol) {
mol.delete();
}
}
assert.equal(molList.size(), 2);
let i = 0;
while (!molList.at_end()) {
try {
mol = molList.next();
} finally {
if (mol) {
++i;
mol.delete();
}
}
}
assert.equal(i, 2);
assert(molList.at_end());
try {
mol = molList.pop(0);
assert.equal(mol.get_num_atoms(), 4);
} finally {
if (mol) {
mol.delete();
}
}
assert.equal(molList.size(), 1);
assert(molList.at_end());
try {
mol = molList.pop(0);
assert.equal(mol.get_num_atoms(), 5);
} finally {
if (mol) {
mol.delete();
}
}
assert.equal(molList.size(), 0);
assert(molList.at_end());
assert(!molList.pop(0));
try {
mol = RDKitModule.get_mol('C1CCCCC1');
assert(mol);
molList.append(mol);
assert.equal(molList.size(), 1);
assert(!molList.at_end());
} finally {
if (mol) {
mol.delete();
}
}
assert(!molList.at(1));
try {
mol = molList.at(0);
assert(mol);
assert(mol.get_num_atoms(), 6);
} finally {
if (mol) {
mol.delete();
}
}
} finally {
if (molList) {
molList.delete();
}
}
}
function test_mcs() {
{
const smiArray = [
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)oc2cc1 CHEMBL1479679",
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1333382",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)nc2cc1 CHEMBL1437584",
"COc1c(NC(=O)CSc2ccc(Cl)cc2)cc(-c2nc3ccccc3o2)cc1 CHEMBL1601350",
"Cc1cc2nc(-c3cccc(NC(=O)CSc4ccc(Cl)cc4)c3)oc2cc1C CHEMBL1398008",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)nc2cc1 CHEMBL1612903",
"COc1cc2nc(-c3cc(NC(=O)Cc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1316483",
"Cc1c(NC(=O)CSc2ccc(Cl)cc2)cccc1-c1nc2cc(Cl)ccc2o1 CHEMBL1568754",
"COc1ccc2oc(-c3ccc(C)c(NC(=O)COc4cc(C)cc(C)c4)c3)nc2c1 CHEMBL1436972",
"Cc1ccc(SCC(=O)Nc2cc(-c3nc4cc(C)ccc4o3)c(O)cc2)cc1 CHEMBL1611932",
];
let molList;
let mcsSmarts;
try {
molList = molListFromSmiArray(smiArray);
let mcsMol;
try {
mcsMol = RDKitModule.get_mcs_as_mol(molList);
assert(mcsMol);
assert.equal(mcsMol.get_smarts(), '[#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1');
mcsSmarts = RDKitModule.get_mcs_as_smarts(molList);
} finally {
if (mcsMol) {
mcsMol.delete();
}
}
} finally {
if (molList) {
molList.delete();
}
}
assert(mcsSmarts);
assert.equal(mcsSmarts, '[#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1');
}
{
const smiArray = ["C1CC1N2CC2", "C1CC1N"];
let molList;
try {
molList = molListFromSmiArray(smiArray);
let mcsMol;
try {
mcsMol = RDKitModule.get_mcs_as_mol(molList);
assert(mcsMol);
assert.equal(mcsMol.get_num_atoms(), 4);
assert.equal(mcsMol.get_num_bonds(), 4);
} finally {
if (mcsMol) {
mcsMol.delete();
}
}
try {
mcsMol = RDKitModule.get_mcs_as_mol(molList, JSON.stringify({ RingMatchesRingOnly: true }));
assert(mcsMol);
assert.equal(mcsMol.get_num_atoms(), 3);
assert.equal(mcsMol.get_num_bonds(), 3);
} finally {
if (mcsMol) {
mcsMol.delete();
}
}
} finally {
if (molList) {
molList.delete();
}
}
}
{
const smiArray = ["NC1CCCCC1", "Cc1ccccc1", "Cc1cnccc1", "CC1CCCCN1"];
let molList;
const res = new Set();
try {
molList = molListFromSmiArray(smiArray);
["Elements", "Any"].forEach((AtomCompare) => {
["Order", "OrderExact"].forEach((BondCompare) => {
const details = {
AtomCompare,
BondCompare
};
let mcsSmarts;
mcsSmarts = RDKitModule.get_mcs_as_smarts(molList, JSON.stringify(details));
assert(mcsSmarts);
res.add(mcsSmarts);
});
});
} finally {
if (molList) {
molList.delete();
}
}
assert(res.size === 4);
}
{
const smiArray = [
"c1cccc(c12)ccc(c2)-c3n(CCC[NH3+])c(nn3)SCCc4c[nH]c(c45)cccc5",
"c1cccc(c12)sc(c2)-c3n(CCCC[NH3+])c(nn3)SCCc4c[nH]c(c45)cccc5",
];
let molList;
let mcs;
try {
molList = molListFromSmiArray(smiArray);
mcs = RDKitModule.get_mcs_as_json(molList, JSON.stringify({
RingMatchesRingOnly: true,
CompleteRingsOnly: true,
BondCompare: 'Any',
AtomCompare: 'Any',
Timeout: 1,
}));
} finally {
if (molList) {
molList.delete();
}
}
assert(mcs);
mcs = JSON.parse(mcs);
assert(mcs.canceled);
}
{
const smiArray = [
"Nc1ccc(cc1)C-Cc1c(N)cccc1",
"Nc1ccc(cc1)C=Cc1c(N)cccc1",
];
let molList;
let mcs;
try {
molList = molListFromSmiArray(smiArray);
mcs = RDKitModule.get_mcs_as_json(molList);
} finally {
if (molList) {
molList.delete();
}
}
assert(mcs);
mcs = JSON.parse(mcs);
assert(!mcs.canceled);
assert(!Array.isArray(mcs.smarts));
assert(mcs.numAtoms === 8);
assert(mcs.numBonds === 8);
assert(mcs.smarts === '[#7]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]');
try {
molList = molListFromSmiArray(smiArray);
mcs = RDKitModule.get_mcs_as_json(molList, JSON.stringify({StoreAll: true}));
} finally {
if (molList) {
molList.delete();
}
}
assert(mcs);
mcs = JSON.parse(mcs);
assert(!mcs.canceled);
assert(Array.isArray(mcs.smarts));
assert(mcs.numAtoms === 8);
assert(mcs.numBonds === 8);
assert(mcs.smarts.length === 2);
assert(mcs.smarts.includes('[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#7]'));
assert(mcs.smarts.includes('[#7]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]'));
}
{
const smiArray = [
"C1CC1",
"c1ccccc1",
];
let molList;
let mcs;
try {
molList = molListFromSmiArray(smiArray);
mcs = RDKitModule.get_mcs_as_json(molList, JSON.stringify({ CompleteRingsOnly: true }));
} finally {
if (molList) {
molList.delete();
}
}
assert(mcs);
mcs = JSON.parse(mcs);
assert(!mcs.canceled);
assert(!mcs.numAtoms);
assert(!mcs.numBonds);
assert(!mcs.smarts);
try {
molList = molListFromSmiArray(smiArray);
mcs = RDKitModule.get_mcs_as_json(molList, JSON.stringify({ CompleteRingsOnly: true, StoreAll: true }));
} finally {
if (molList) {
molList.delete();
}
}
assert(mcs);
mcs = JSON.parse(mcs);
assert(!mcs.canceled);
assert(!mcs.numAtoms);
assert(!mcs.numBonds);
assert(!mcs.smarts.length);
}
}
function test_get_num_atoms_bonds() {
var mol = RDKitModule.get_mol('CCCC');
var molH = RDKitModule.get_mol_copy(mol);
molH.add_hs_in_place();
assert.equal(mol.get_num_atoms(), molH.get_num_atoms(true));
assert.equal(mol.get_num_atoms(), 4);
assert.equal(molH.get_num_atoms(), 14);
assert.equal(molH.get_num_atoms(false), 14);
assert.equal(mol.get_num_bonds(), 3);
assert.equal(molH.get_num_bonds(), 13);
}
function test_sanitize_no_kekulize_no_setaromaticity() {
var molblock1 = `
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END`;
var molblock2 = `
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 2 0
5 6 1 0
6 1 2 0
M END`;
var mol1 = RDKitModule.get_mol(molblock1, JSON.stringify({kekulize: false, setAromaticity: false}));
var mol2 = RDKitModule.get_mol(molblock2, JSON.stringify({kekulize: false, setAromaticity: false}));
assert.notEqual(mol1.get_molblock(), mol2.get_molblock());
mol1.delete();
mol2.delete();
mol1 = RDKitModule.get_mol(molblock1);
mol2 = RDKitModule.get_mol(molblock2);
assert.equal(mol1.get_molblock(), mol2.get_molblock());
mol1.delete();
mol2.delete();
}
function test_partial_sanitization() {
var mol1 = RDKitModule.get_mol('C1CCC2CCCC2C1', JSON.stringify({
sanitize: false, removeHs: false, assignStereo: false,
}));
var fp1 = mol1.get_morgan_fp(JSON.stringify({radius: 2, nBits: 32}));
assert.equal(fp1, '00001001010101000000100000110010');
mol1.delete();
var mol2 = RDKitModule.get_mol('C1CCC2CCCC2C1', JSON.stringify({
sanitize: false, removeHs: false, assignStereo: false, fastFindRings: false
}));
var exceptionThrown = false;
try {
mol2.get_morgan_fp(JSON.stringify({radius: 2, nBits: 32}));
} catch (e) {
exceptionThrown = true;
}
assert(exceptionThrown);
mol2.delete();
}
function test_capture_logs() {
["set_log_tee", "set_log_capture"].forEach((func, i) => {
console.log(`${i + 1}. ${func}`);
var logHandle = RDKitModule[func]("dummy");
assert(!logHandle);
var logHandle = RDKitModule[func]("rdApp.*");
assert(logHandle);
var logBuffer = logHandle.get_buffer();
assert(!logBuffer);
var mol = RDKitModule.get_mol("CN(C)(C)C");
assert(!mol);
logBuffer = logHandle.get_buffer();
assert(logBuffer);
assert(logBuffer.includes('Explicit valence for atom # 1 N, 4, is greater than permitted'));
logHandle.clear_buffer();
assert(!logHandle.get_buffer());
logHandle.delete();
})
}
function test_rgroup_match_heavy_hydro_none_charged() {
var templateRef = RDKitModule.get_mol(`
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-0.5804 1.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2948 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2948 -0.0330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5804 -0.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1340 -0.0330 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
0.1340 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8485 -0.4455 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
6 1 1 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 7 1 0 0 0 0
M RGP 1 7 1
M END
`);
assert(templateRef);
var mol;
var allowRGroups = true;
[true, false].forEach((alignOnly) => {
mol = RDKitModule.get_mol("Cc1ccccc1");
assert(mol);
assert.equal(mol.get_num_atoms(), 7);
assert.equal(JSON.parse(mol.generate_aligned_coords(templateRef, JSON.stringify({ allowRGroups, alignOnly }))).atoms.length, 7);
mol.delete();
mol = RDKitModule.get_mol("c1ccccc1");
assert(mol);
assert.equal(mol.get_num_atoms(), 6);
assert.equal(JSON.parse(mol.generate_aligned_coords(templateRef, JSON.stringify({ allowRGroups, alignOnly }))).atoms.length, 6);
mol.delete();
mol = RDKitModule.get_mol("[H]c1ccccc1", JSON.stringify({removeHs: false}));
assert(mol);
assert.equal(mol.get_num_atoms(), 7);
assert.equal(JSON.parse(mol.generate_aligned_coords(templateRef, JSON.stringify({ allowRGroups, alignOnly }))).atoms.length, 7);
mol.delete();
mol = RDKitModule.get_mol("n1ccccc1");
assert(mol);
assert.equal(mol.get_num_atoms(), 6);
assert.equal(JSON.parse(mol.generate_aligned_coords(templateRef, JSON.stringify({ allowRGroups, alignOnly }))).atoms.length, 6);
mol.delete();
mol = RDKitModule.get_mol("C[n+]1ccccc1");
assert(mol);
assert.equal(mol.get_num_atoms(), 7);
assert.equal(JSON.parse(mol.generate_aligned_coords(templateRef, JSON.stringify({ allowRGroups, alignOnly }))).atoms.length, 7);
mol.delete();
});
templateRef.delete();
}
function test_get_sss_json() {
var fentanylScaffold = RDKitModule.get_mol(`
MJ201100
25 27 0 0 0 0 0 0 0 0999 V2000
-0.3910 -1.2720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2160 -1.2721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6285 -1.9866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2161 -2.7010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3911 -2.7011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0214 -1.9865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0213 -0.5575 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.3911 0.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0213 0.8713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3911 1.5859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2161 1.5858 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.6287 0.8714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2161 0.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6286 2.3002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8463 -0.5575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2588 0.1569 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.4536 2.3002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8661 1.5858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6910 1.5858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1036 0.8712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6912 0.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8662 0.1567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4536 0.8713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2589 -1.2720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0839 -1.2719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
9 10 1 0 0 0 0
12 13 1 0 0 0 0
8 9 1 0 0 0 0
8 13 1 0 0 0 0
10 11 1 0 0 0 0
11 12 1 0 0 0 0
11 14 1 0 0 0 0
1 7 1 0 0 0 0
7 8 1 0 0 0 0
7 15 1 0 0 0 0
14 17 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
20 21 2 0 0 0 0
21 22 1 0 0 0 0
22 23 2 0 0 0 0
18 19 2 0 0 0 0
23 18 1 0 0 0 0
15 24 1 0 0 0 0
24 25 1 0 0 0 0
15 16 2 0 0 0 0
M END
`);
var bilastine = RDKitModule.get_mol("O=C(O)C(c1ccc(cc1)CCN4CCC(c2nc3ccccc3n2CCOCC)CC4)(C)C");
var referenceSmarts = "c1ccccc1CCN1CCCCC1";
var res = bilastine.generate_aligned_coords(fentanylScaffold, JSON.stringify({useCoordGen: true, referenceSmarts}));
assert(res);
var resExpected = "{\"atoms\":[6,5,4,9,8,7,10,11,12,13,14,15,30,31],\"bonds\":[13,30,14,29,12,36,11,10,9,5,4,33,8,6,7]}";
assert.equal(res, resExpected);
assert.equal(JSON.parse(res).bonds.length, 15);
bilastine.delete();
fentanylScaffold.delete();
}
function test_relabel_mapped_dummies() {
var core = RDKitModule.get_mol("c1cc([4*:2])c([3*:1])cn1");
assert.equal(core.get_cxsmiles(), "c1cc([4*:2])c([3*:1])cn1 |atomProp:3.dummyLabel.*:3.molAtomMapNumber.2:5.dummyLabel.*:5.molAtomMapNumber.1|");
core.delete();
core = RDKitModule.get_mol("c1cc([4*:2])c([3*:1])cn1", JSON.stringify({mappedDummiesAreRGroups: true}));
assert.equal(core.get_cxsmiles(), "*c1ccncc1* |atomProp:0.dummyLabel.R2:7.dummyLabel.R1|");
core.delete();
}
function test_assign_cip_labels() {
var origSetting;
const getTextSection = (svg) => (
svg.split('\n').map((line) => line.replace(/^<text.+>([^<]*)<\/text>$/, '$1')).join('')
);
try {
origSetting = RDKitModule.use_legacy_stereo_perception(true);
{
var mol = RDKitModule.get_mol('C/C=C/c1ccccc1[S@@](C)=O');
var svg = mol.get_svg_with_highlights(JSON.stringify({noFreetype: true, addStereoAnnotation: true}));
assert(getTextSection(svg).includes("(S)"));
assert(!getTextSection(svg).includes("(R)"));
mol.delete();
}
RDKitModule.use_legacy_stereo_perception(false);
{
var mol = RDKitModule.get_mol('C/C=C/c1ccccc1[S@@](C)=O');
var svg = mol.get_svg_with_highlights(JSON.stringify({noFreetype: true, addStereoAnnotation: true}));
assert(!getTextSection(svg).includes("(S)"));
assert(!getTextSection(svg).includes("(R)"));
mol.delete();
}
{
var mol = RDKitModule.get_mol('C/C=C/c1ccccc1[S@@](C)=O', JSON.stringify({assignCIPLabels: true}));
var svg = mol.get_svg_with_highlights(JSON.stringify({noFreetype: true, addStereoAnnotation: true}));
assert(!getTextSection(svg).includes("(S)"));
assert(getTextSection(svg).includes("(R)"));
mol.delete();
}
} finally {
RDKitModule.use_legacy_stereo_perception(origSetting);
}
}
function test_smiles_smarts_params() {
{
const amoxicillinPubChem = 'CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=C(C=C3)O)N)C(=O)O)C';
const mol = RDKitModule.get_mol(amoxicillinPubChem);
{
const canonicalSmiles = mol.get_smiles();
assert(canonicalSmiles === 'CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(=O)O');
}
['{}', ''].forEach((emptyJson) => {
const canonicalSmiles = mol.get_smiles(emptyJson);
assert(canonicalSmiles === 'CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(=O)O');
});
const nonCanonicalSmiles = mol.get_smiles(JSON.stringify({canonical: false}));
assert(nonCanonicalSmiles === 'CC1(C)[C@H](C(=O)O)N2[C@H](S1)[C@H](NC(=O)[C@@H](c1ccc(O)cc1)N)C2=O');
const canonicalSmilesNoStereo = mol.get_smiles(JSON.stringify({doIsomericSmiles: false}));
assert(canonicalSmilesNoStereo === 'CC1(C)SC2C(NC(=O)C(N)c3ccc(O)cc3)C(=O)N2C1C(=O)O');
const nonCanonicalSmilesNoStereo = mol.get_smiles(JSON.stringify({doIsomericSmiles: false, canonical: false}));
assert(nonCanonicalSmilesNoStereo === 'CC1(C)C(C(=O)O)N2C(S1)C(NC(=O)C(c1ccc(O)cc1)N)C2=O');
mol.delete();
}
{
const bicyclo221heptane = `
RDKit 2D
9 10 0 0 1 0 0 0 0 0999 V2000
-2.8237 -1.3088 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.5723 -0.3996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5723 1.1473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1011 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3701 1.1474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3701 -0.3995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6217 -1.3087 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.1009 -0.8775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 0.3739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
4 3 1 0
4 5 1 0
6 5 1 0
6 7 1 1
6 8 1 0
8 9 1 1
8 2 1 0
4 9 1 1
M END
`;
const mol = RDKitModule.get_mol(bicyclo221heptane);
{
const canonicalCXSmiles = mol.get_cxsmiles();
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wD:3.9,wU:1.0,5.4,6.7');
}
['{}', ''].forEach((emptyJson) => {
const canonicalCXSmiles = mol.get_cxsmiles(emptyJson);
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wD:3.9,wU:1.0,5.4,6.7');
});
{
const canonicalCXSmiles = mol.get_cxsmiles(JSON.stringify({restoreBondDirOption: 'RestoreBondDirOptionTrue'}));
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wU:1.0,3.3,5.4,6.7');
}
{
const nonCanonicalCXSmilesNoStereo = mol.get_cxsmiles(JSON.stringify({doIsomericSmiles: false, canonical: false, CX_ALL_BUT_COORDS: true}));
assert(nonCanonicalCXSmilesNoStereo === 'OC1CC2CC(N)C1C2');
const nonCanonicalCXSmilesNoStereoAtomProp = `${nonCanonicalCXSmilesNoStereo} |atomProp:1.atomProp.1&#46;234|`;
const molWithAtomProp = RDKitModule.get_mol(nonCanonicalCXSmilesNoStereoAtomProp);
assert(molWithAtomProp);
const cxSmilesWithAtomProp = molWithAtomProp.get_cxsmiles(JSON.stringify({CX_ALL_BUT_COORDS: true}));
assert(cxSmilesWithAtomProp === 'NC1CC2CC(O)C1C2 |atomProp:5.atomProp.1&#46;234|');
molWithAtomProp.delete();
}
mol.delete();
}
{
const chiralQuery = RDKitModule.get_qmol('N-[C@H](-C(-O)=O)-C(-C)-C');
assert(chiralQuery.get_smarts() === 'N-[C@&H1](-C(-O)=O)-C(-C)-C');
['', '{}'].forEach((emptyJson) => {
assert(chiralQuery.get_smarts(emptyJson) === 'N-[C@&H1](-C(-O)=O)-C(-C)-C');
});
assert(chiralQuery.get_smarts(JSON.stringify({doIsomericSmiles: false})) === 'N-[C&H1](-C(-O)=O)-C(-C)-C');
}
{
const chiralQuery = RDKitModule.get_qmol('N-[C@H](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
assert(chiralQuery.get_cxsmarts() === 'N-[C@&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
['', '{}'].forEach((emptyJson) => {
assert(chiralQuery.get_cxsmarts(emptyJson) === 'N-[C@&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
});
assert(chiralQuery.get_cxsmarts(JSON.stringify({doIsomericSmiles: false})) === 'N-[C&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
}
}
function test_wedged_bond_atropisomer() {
var atropisomer = `
Mrv2311 05242408162D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.0006 -1.54 0 0
M V30 2 N 2.0006 -3.08 0 0
M V30 3 C 0.6669 -3.85 0 0
M V30 4 C -0.6668 -3.08 0 0
M V30 5 C -0.6668 -1.54 0 0
M V30 6 C -2.0006 -0.77 0 0
M V30 7 C 0.6669 -0.77 0 0
M V30 8 C 0.6669 0.77 0 0
M V30 9 C -0.6668 1.54 0 0
M V30 10 C -2.0006 0.77 0 0
M V30 11 C -0.6668 3.08 0 0
M V30 12 C 0.6669 3.85 0 0
M V30 13 C 2.0006 3.08 0 0
M V30 14 C 2.0006 1.54 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 1 7 5 CFG=3
M V30 7 2 7 1
M V30 8 1 7 8
M V30 9 2 8 9
M V30 10 1 9 10
M V30 11 1 9 11
M V30 12 2 11 12
M V30 13 1 12 13
M V30 14 2 13 14
M V30 15 1 8 14
M V30 END BOND
M V30 END CTAB
M END
`;
var mol = RDKitModule.get_mol(atropisomer);
assert(mol);
var svg = mol.get_svg_with_highlights(JSON.stringify({
useMolBlockWedging: true, noFreetype: true
}));
assert(svg.match(/<path class='bond-5 atom-6 atom-4'.*style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1\.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' \/>/g).length > 6);
assert(!svg.match(/<path class='bond-5 atom-6 atom-4'.*style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2\.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' \/>/g));
mol.delete();
}
function test_get_molblock_use_molblock_wedging() {
var mb = `
RDKit 2D
9 10 0 0 1 0 0 0 0 0999 V2000
1.4885 -4.5513 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.0405 -3.9382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8610 -4.0244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1965 -3.2707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0250 -2.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2045 -2.3775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7920 -1.6630 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.8690 -3.1311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5834 -2.7186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
4 3 1 0
4 5 1 0
6 5 1 0
6 7 1 1
6 8 1 0
8 9 1 1
8 2 1 0
4 9 1 1
M END
`;
var mol = RDKitModule.get_mol(mb);
assert(mol);
var molCopy = RDKitModule.get_mol_copy(mol);
assert(molCopy);
var mbRDKitWedging = mol.get_molblock();
assert(mbRDKitWedging !== mb);
var mbOrigWedging = mol.get_molblock(JSON.stringify({useMolBlockWedging: true}));
assert(mb === mbOrigWedging);
var mbRDKitWedgingPostOrig = mol.get_molblock();
assert(mb !== mbRDKitWedgingPostOrig);
assert(mbRDKitWedging === mbRDKitWedgingPostOrig);
mol.delete();
}
initRDKitModule().then(function(instance) {
var done = {};
const waitAllTestsFinished = () => {
const poll = resolve => {
if (Object.values(done).every(v => v)) {
resolve();
} else {
setTimeout(() => poll(resolve), 100);
}
}
return new Promise(poll);
}
RDKitModule = instance;
console.log(RDKitModule.version());
test_basics();
test_molblock_nostrict();
test_molblock_rgp();
test_get_aromatic_kekule_form();
test_sketcher_services();
test_sketcher_services2();
test_abbreviations();
if (RDKitModule.SubstructLibrary) {
test_substruct_library(done);
test_substruct_library_merge_hs();
test_substruct_library_empty_mols();
test_substruct_library_empty_lib();
test_substruct_library_empty_query();
}
test_generate_aligned_coords();
test_isotope_labels();
test_generate_aligned_coords_allow_rgroups();
test_generate_aligned_coords_accept_failure();
test_generate_aligned_coords_align_only();
test_get_mol_no_kekulize();
test_get_smarts();
test_get_cxsmarts();
test_has_coords();
test_kekulize();
test_sanitize();
test_removehs();
test_normalize_depiction();
test_straighten_depiction();
test_flexicanvas();
if (RDKitModule.get_rxn) {
test_rxn_drawing();
test_run_reaction();
}
test_legacy_stereochem();
test_allow_non_tetrahedral_chirality();
test_prop();
test_highlights();
test_add_chiral_hs();
test_wedging_all_within_scaffold();
test_wedging_outside_scaffold();
test_wedging_if_no_match();
test_get_frags();
if (RDKitModule.Mol.prototype.get_mmpa_frags) {
test_get_mmpa_frags();
}
test_hs_in_place();
test_query_colour();
test_alignment_r_groups_aromatic_ring();
test_is_valid_deprecated();
test_mol_list();
test_get_num_atoms_bonds();
if (RDKitModule.get_mcs_as_mol) {
test_mcs();
}
test_sanitize_no_kekulize_no_setaromaticity();
test_partial_sanitization();
test_capture_logs();
test_rgroup_match_heavy_hydro_none_charged();
test_get_sss_json();
test_relabel_mapped_dummies();
test_assign_cip_labels();
test_smiles_smarts_params();
test_wedged_bond_atropisomer();
test_get_molblock_use_molblock_wedging();
waitAllTestsFinished().then(() =>
console.log("Tests finished successfully")
);
});
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